Otago researcher takes genomic sequencing to the farm to help transform lives

International scientists, including a University of Otago researcher, in a world first have used whole genome sequencing to help diagnose a plant pathogen destroying crops on African farms, potentially paving the way for preventing crop failures, vital to the African economy.

Dr Jo-Ann Stanton, a Senior Research Fellow in the University of Otago’s Department of Anatomy, helped develop the PDQeX, one of the two prototype technologies which have made it possible to carry out the whole genome sequencing on remote African farms.

“This achievement opens the way to rapid and accurate pathogen identification, permitting immediate corrective action to prevent crop failure,” Dr Stanton explains.

“For the subsistence farmers of East Africa this is the difference between having food and an income or going hungry,” she says.

“Crop failure means a loss of food security and no income for school fees, supplies, farm improvements or maintenance.”

The team including scientists from Mikocheni Agricultural Research Institute in Tanzania, the National Crops Resources Research Institute in Uganda, Jomo Kenyatta University of Agriculture and Technnology in Kenya and the University of Western Australia worked together under the “Cassava Virus Action Project” with cassava growers in three countries: Tanzania, Uganda and Kenya.

Cassava, a tuberous root of a tropical tree which produces flour and a starchy vegetable similar to potato, is under attack from viral pathogens that reduce or destroy the crop. Farmers affected by the growing viral threat depend on cassava for their main food source and yearly income.

“800 million people worldwide depend on cassava as their main source of calories and virus spread is a significant global threat,” Dr Stanton says.

As a researcher her vision is to take complex molecular diagnostics out of the lab and into the hands of non-experts to facilitate rapid, accurate and cost-effective responses to real-life situations. This project is achieving exactly that, she says.

Using hand-held molecular diagnostic devices, Dr Stanton and the team has been able to carry out whole genome sequencing on the farms. A device (PDQeX) from New Zealand company ZyGEM that permits on-site DNA extraction, was used together with the MinIT base-calling mini-supercomputer made by UK company, Oxford Nanopore.

Bringing these technologies together with the MinION, a portable DNA sequencer, it was possible to select either leaf, stem or insect samples on the farms, prepare the DNA for sequencing and then covert raw data to DNA sequence reads for data interpretation, all in real time.

Dr Stanton says the whole process took less than four hours from sampling to diagnostic results and all devices were run on battery working outdoors at the farms.

The project has significant implications not only for the African farmers, she says.

On a broader level, this breakthrough has applications in areas of human and animal health, environmental management and conservation.

The need for accurate, rapid and on-site diagnosis is growing as the globalisation of human activity accelerates.

Source: University of Otago

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MPI invites thoughts on dairy herd improvement regulatory regime

The Ministry for Primary Industries (MPI) wants to hear from the dairy industry and people with an interest in how the dairy herd improvement regulatory regime can help to ensure that New Zealand’s dairy industry remains world leading.

The dairy herd improvement regulatory regime has not been comprehensively reviewed since it was established in 2001, says Emma Taylor, MPI’s director of agriculture, marine and plant policy.

“It’s important the dairy herd improvement regulatory regime reflects the changing needs of the dairy industry. It’s timely to look at how the regulatory settings can better support industry both now and into the future.

“Dairy herd improvement adds substantial value to New Zealand’s dairy industry, estimated at around $300 million each year.”

Farmers have been testing samples of milk from their dairy cattle and recording data to inform their herd management decisions for over a century. For industry to achieve optimal rates of genetic gain, it needs a comprehensive, accurate, and continuous supply of data to inform decisions on herd management and breeding.

“The regulatory regime contributes to the breeding of more productive dairy animals through herd testing, herd recording, animal evaluation and artificial breeding. It also has the potential to support better environmental and animal health outcomes,” says Emma Taylor.

“We want to hear from people about how the regulatory regime can more effectively support the performance of the dairy industry. We also want to hear from industry on the effects of changing technology and the future implications on the dairy herd improvement sector.”

The six-week consultation will run from October 1 to 5pm November 12.

Find out about the consultation and have your say HERE.

Source: Ministry for Primary Industries 

Mozzies knocked out with gene drive – media centre gathers expert reaction

The Science Research Centre has published expert comment after UK researchers reported they had successfully used a CRISPR-based gene drive to cause the collapse of a population of caged malaria-carrying mosquitoes.

The study, published today, targeted a gene that determines whether an individual mosquito develops as a male or a female. Previous attempts have been thwarted by the mosquitoes developing resistance to the gene drive, but the researchers say this didn’t happen and within eight generations no females were being produced and the population collapsed.

The NZ Science Media Centre also has published comments gathered by the Australian Science Media Centre.

Joint comment – Professor Peter Dearden and Professor Neil Gemmell, University of Otago:

The paper by Kyrou et al. is an interesting and important step forward in the development of gene drive technologies. These technologies may make possible the extinction of a population of a pest, or as here, a disease-carrying organism using genetic techniques. This paper describes a gene drive system, used in a contained lab experiment, that drives the extinction of a malaria-carrying mosquito.

The reason this paper is a step forward is that the target gene chosen in this manuscript allows the authors to solve one of the problems with gene drives, which is the development of resistance. By targeting a gene involved in specifying the sex of mosquitos, they have ensured that when resistance arises it leads to female infertility, and is selected against.

The gene drive has little to no effect in males, meaning that while females are sterile, the males keep spreading the gene drive mechanism, leading to more infertile females and finally population collapse.

The gene targeted is present in most insects and acts in a similar way, indeed this similar approach has been proposed as a technology for wasp control in New Zealand.

The authors state that they believe that such mosquitos might be available for release to the wild in 5-8 years, and that there is a lot of research and testing to be done before then. One missing aspect of this approach is a technology that allows a gene drive to be turned off or limited once released, something that needs to be investigated.

The timeline for developing these mosquitos is a strong signal that work on gene drive systems for pests in New Zealand will take a long time without significant investment. Currently there is some disquiet about such work, and we need to continue to pursue such research in contained labs to understand the risks and benefits if we are to ever be in a position to trial such tools for the control of our pests, whether it is wasps, rats, or something new that threatens our economy or health.

Professor Ary Hoffmann is Director of Research at the Centre for Environmental Stress and Adaptation Research, University of Melbourne

This is an interesting development in the potential use of gene drive systems to suppress pest populations.

In particular, the authors target the essential doublesex gene that is involved in the sex determination pathway and needed for normal development of males and females. A construct was developed that prevents females developing normally and results in them producing a sharply reduced number of viable eggs. This construct could be driven through the population, and importantly appears to be stable so far – it has proven resistant to the rapid evolution of genetic variants that stop the gene drive acting.

Importantly, the work shows that there is a very rapid decrease in egg number in population cages such that populations of Anopheles mosquitoes eventually collapse.

It remains to be seen if the same phenomenon can be reproduced in large cages designed to represent field populations more closely where there is a greater chance of mutations arising that prevent the gene drive from operating properly.

Nevertheless, at least in the short term, the experiments show that it is possible to produce a stable drive to suppress populations of mosquito disease vectors.

Ary has not declared any conflicts of interest.

Dr Gordana Rasic is a senior research officer in the Mosquito Control Group, QIMR Berghofer Medical Research Institute

In this study, scientists created a new gene drive that disrupts development of female malarial mosquitoes (Anopheles gambiae) and causes their caged populations to crash.

Andrea Crisanti’s group at Imperial College, UK has used CRISPR technology to create a mutation in a gene (doublesex) that prevents normal development of biting females but does not affect harmless male mosquitoes.

By linking the mutation to a CRISPR-based machinery that ensures it is transmitted nearly 100 per cent of the time, the mutation quickly spreads through a population, turning more and more females into intersex mosquitoes that can’t bite and reproduce.

The heavy hit on egg production was enough to cause total collapse of experimental caged populations in less than a year.

This is not the first gene drive for suppression of malarial mosquitoes that Crisanti’s group has created, but the doublesex construct seems much more resilient to mosquitoes developing resistance to it, and this is what gives hope it might work in the field.

Field trials are indeed the ultimate test for the efficacy of suppression gene drives, but the releases of such GM mosquitoes are met with heavy regulatory constraints and public skepticism.

An important breakthrough happened this August, when Burkina Faso’s national biosafety authority granted permission to release 10,000 non-gene-drive GM Anopheles mosquitoes, as a first step towards eventual rollout of the gene drive constructs like Crisanti’s.

Exciting and hopeful times in fight against malaria are ahead.

Gordana has not declared any conflicts of interest.

Dr Cameron Webb is a Clinical Lecturer with the University of Sydney

Novel approaches to mosquito control are critical if we are to reduce the burden of mosquito-borne disease. Traditional approaches to controlling mosquitoes, especially the use of insecticides, is becoming less effective as key mosquitoes involved in outbreaks of disease are becoming resistant to our commonly-used insecticides.

As malaria is still responsible for killing over half a million people every year and making hundreds of millions of people sick, new technologies are required to battle mosquito-borne disease.

While gene drives have shown great potential in the past, laboratory studies have demonstrated that resistance in mosquitoes to these approaches developed in much the same way that they’re beating our commonly-used insecticides.

This new research, however, opens new potential applications of this strategy and provides support for researchers to pursue field-based studies. No such resistance to this approach was shown in these newly published laboratory studies.

By releasing laboratory-reared, genetically-modified mosquitoes into the field, they can crash the local mosquito populations by reducing the proportion of fertile female mosquitoes. It is a tantalising prospect that collapsing mosquito populations may substantially reduce the transmission of mosquito-borne pathogens.

This latest research demonstrates great potential for future management of malaria in many parts of the world, especially Africa.

However, adapting this approach to Australian mosquito-borne disease may face many challenges. Australia is free of malaria but thousands of people fall ill following mosquito bites each summer.

Unfortunately, there are many different types of mosquito, found in many different types of environments, that drive outbreaks of mosquito-borne disease here.

The release of genetically modified mosquitoes is still a long way off but perhaps in the future it will be an additional tool available to local health authorities in reducing the public health risks associated with our local mosquitoes.

Cameron has not declared any conflicts of interest. 

Source:  Science Media Centre

The breed could be right on the tip of a calf’s tongue

Massey University research suggests their tongues may hold a clue to identifying the breed of a new-born calf.

The New Zealand dairy herd is comprised predominantly of Holstein-Friesian, Jersey and Holstein-Friesian-Jersey crossbreed cattle.

A Jersey calf is easy to identify but both the Angus-cross and Holstein-Friesian-Jersey calves may have a completely black coat, making it difficult to identify the breed of new-born calves.

Research aimed at finding if tongue colour could be a useful predictor of breed in Angus-cross-dairy and dairy-breed calves was led by PhD student Lucy Coleman after an Angus breeder noticed the tongue colour trend.

“Identifying the breed of calf prior to four days of age is important, so that the dairy farmer is able to retain appropriate dairy-breed heifers as replacements, and dairy-beef calf rearers are able to purchase beef-cross calves for rearing. The best option for identifying breed is DNA testing for parentage. However, this is expensive, and results take longer than four days to obtain,” she says.

“Holstein-Friesian cattle possess a gene which causes the white patches in the coat and a pink coloured tongue, whereas Angus and Jersey cattle lack this gene and have black tongues. So we wanted to see if the colour of their tongues could be an indicator of breed.”

An initial study of the tongue-colour of 476 Angus-cross-dairy and dairy calves shortly after birth was conducted as part of Miss Coleman’s PhD project.

The findings showed that selecting calves to rear for beef solely on having a black-coloured tongue, would correctly identify 73 per cent of Angus-cross calves, and 90 per cent of dairy-breed calves.

“The initial study provided useful clues for breed identification, however was not infallible as the occurrence of spotted tongues raised an issue of whether to keep or sell that calf,” Miss Coleman says.

A second study was conducted the following year, recording the presence of horns and tongue colour of 418 Angus-cross-dairy and dairy calves. The majority of dairy calves (95 per cent) had horn buds present at birth, while none of the Angus-cross calves had horn buds, indicating that horns were exclusive to the dairy breed calves.

The outcome of the second study, provided separate recommendations for dairy farmers, and calf-rearers buying beef-cross-dairy calves.

Dairy farmers should keep only calves with horn buds as replacement dairy heifers, meaning no Angus-cross calves would be incorrectly identified and kept.

For calf rearers, the recommendation was to buy only calves without horn buds (polled) and with a black tongue which greatly reduces the chances of inadvertently purchasing dairy breed calves.

The experiments were conducted with calves from the Beef+Lamb NZ Genetics dairy-beef progeny test based at Limestone Downs farm in Port Waikato.

The first study, titled Breed variation in tongue colour of dairy and beef-cross-dairy calves was co-authored by Professor Hugh Blair, Professor Nicolas Lopez-Villalobos, Dr Penny Back and Associate Professor Rebecca Hickson of the School of Agriculture and Environment.

Researchers are poised to win the race against rust diseases

A joint US and Australian research team has generated the first haplotype-resolved genome sequences for the rust fungi causing oat crown rust and wheat stripe rust diseases, two of the most destructive pathogens in oat and wheat, respectively.

After using the latest genome sequencing technologies to understand how rust fungi adapt to overcome resistance in crop varieties, scientists from the University of Minnesota, the USDA-ARS Cereal Disease Laboratory, the Australian National University, Commonwealth Scientific and Industrial Research Organisation (CSIRO) and the University of Sydney are releasing results with two publications in mBio, a journal by the American Society of Microbiology.

The work was announced (here) by the University of Minnesota.

“Like humans, rust fungi contain two copies of each chromosome, which makes their genetics much more complicated than other types of fungi,” said Assistant Professor Melania Figueroa from the University of Minnesota. Figueroa co-led the sequencing effort for the oat crown rust fungus P. coronata f. sp. avenae along with Shahryar Kianian, research leader at the USDA-ARS Cereal Disease Laboratory and adjunct professor at the University of Minnesota.

“A key advance of this work is that for the first time, separate genome assemblies were generated reflecting both of the two chromosome copies in the rust.”

In parallel, Postdoctoral Fellow Benjamin Schwessinger and Professor John Rathjen at the Australian National University applied similar approaches to develop an improved genome assembly of the stripe rust fungus, P. striiformis f. sp. tritici. By working together the two teams were able to combine their techniques and knowledge to achieve these breakthroughs much more rapidly than by working alone.

These studies represent a breakthrough in plant pathology as they now show how genetic diversity between the two chromosome copies can influence the emergence of new virulent pathogen strains.

Both studies uncovered a surprisingly high level of diversity between the two copies, suggesting that such variation likely serves as the basis to rapidly evolve new rust strains.

“Reports from growers facing yield losses due to oat crown rust occur during most cropping seasons and the genome assemblies of this pathogen will help us understand the evolution of this pathogen and means to develop more resistant crops,” said Kianian, who coordinates annual rust surveys in the US in order to monitor the pathogen population in oat growing areas.

The oat crown rust genomics study compared two strains from North Carolina and South Dakota with different virulent profiles which were obtained in 2012 as part of the routine USDA-ARS Rust Surveys.

The first author of this publication, Marisa Miller, is the awardee of a prestigious USDA-NIFA Postdoctoral Fellow and recently embarked on a study comparing the genomic composition of oat crown rust strains collected in 1990 and 2015.

“In the last 25 years the population of oat crown rust has gained additional virulences, and we would like to understand how this has occurred. Miller’s work is essential to answering this question,” commented Figueroa.

“Oat crown rust is one of the most rapidly evolving rust pathogens,” explained University of Minnesota Adjunct Professor Peter Dodds of CSIRO Agriculture and Food. “So this work will really help understand how new rust diseases like the highly destructive Ug99 race of wheat stem rust can overcome resistance in crops.”

The publications describing the work in the oat crown rust and wheat stripe rust pathogens, both released in the current issue of mBio, will serve as a framework for future studies of virulence evolution in these pathogens as well as for applying similar approaches to the rust fungi causing many other major crop diseases.

Aust researchers’ wheat genes discovery has potential to boost food security

The discovery of genes that determine the yield of flour from wheat could increase milling yield, boosting food security and producing a healthier flour.

University of Queensland researchers believe the discovery could increase the amount of flour produced from wheat by as much as 10 per cent. .

Wheat — the leading temperate climate crop — provides 20 per cent of the total calories and proteins consumed worldwide. Wheat grain is milled, or crushed, to make flour for bread and other food products.

UQ Queensland Alliance for Agriculture and Food Innovation Director Professor Robert Henry said his research team had pinpointed the genes that control a cell protein which acts like a glue, holding the wheat grain’s endosperm, wheat germ and bran layers together.

“Wheats that produce less of this glue-like protein come apart more easily in the milling process,” he said.

“This increases the efficiency of processing and improves the nutritional profile of the flour as more of the outer parts of the endosperm — rich in vitamins and minerals — are incorporated into the flour.

“This applies not only to white flour but also to wholemeal flour.

“Potentially we can take high-yielding field wheats that have not traditionally been considered suitable for milling, and turn them into milling wheats.

“This will improve on-farm production and reduce post-harvest wastage and the amount of resources used to grow the wheat.

“And, by getting a few per cent more flour from the 700 million tonnes of wheat produced globally each year, we will be producing significantly more food from the same amount of wheat,” he said.

Australian wheat traditionally attracts a high price in the market because it has a reputation of giving high flour yields.

“We haven’t been able to genetically select for this trait at early stages of breeding before,” Professor Henry said.

“The effect of this cell adhesion protein explains the difference between wheats that give us 70 per cent flour when we mill it, to 80 per cent, which is quite a big difference.”

Professor Henry said this knowledge could be employed immediately in wheat breeding programs.

“It means that we can produce premium wheats more efficiently and push the yields of quality premium wheats up.”

The team is now looking at DNA testing to breed wheats based on this new molecular discovery. Their findings are published in Scientific Reports.

Cracking manuka’s genetic code may mitigate the effects of myrtle rust

A nationwide science project that sequenced the manuka genome and is now exploring its genetic diversity may be instrumental in protecting the indigenous plant from the fungal disease myrtle rust.

Using state-of-the-art genome sequencing technologies, Plant & Food Research scientists mapped manuka’s genetic blueprint in 2015 and shared the information with tangata whenua and the New Zealand research community.

The research focus has since moved to using bioinformatic techniques to acquire a detailed understanding of the unique attributes of manuka’s genetic stocks – the data have been gleaned from around 1000 samples of manuka leaf collected nationwide in a collaboration with Landcare Research, the University of Waikato and key Maori partners.

The information generated is providing important scientific insights concerning the distribution and genetic diversity within and between manuka populations in New Zealand.

“A key objective of the project has always been to understand how genetic material is exchanged between manuka populations by pollen and seed dispersal to help whānau and hapū, and the honey industry, to develop unique stories around provenance, and help ensure genetic variation for conservation purposes,” says Plant & Food Research Science Group Leader Dr David Chagné.

“With the arrival of myrtle rust on the New Zealand mainland, we soon realised the need for an additional and more specific conservation application for the project.

“While it’s not clear just what effect myrtle rust will have on mānuka under New Zealand conditions, we should expect differences in susceptibility and resistance across the mānuka populations.

“By using the latest technologies for DNA sequencing and new methodologies for bioinformatic data analysis we can determine which parts of the genome are associated with tolerance.

“This will help us to better predict the potential damage from myrtle rust and determine how fast the various mānuka populations will respond to the disease.

“The data will assist with guiding research priorities for maintaining and protecting diversity in mānuka,” says Dr Chagné.

Research results from the project are expected to be released between June and August this year.

The Maori organisations assisting with stakeholder engagement and commercial support in the project are Ngati Porou Miere, Tuhoe Tuawhenua Trust, Atihau-Whanganui, Taitokerau Miere and Tai Tokerau Honey. The project is funded by the Ministry of Business, Innovation and Employment.